Sandbox7 Eric Martz

<font color="red">Please do not edit this page. Thanks, [[User:Eric Martz]], June 26, 2011.</font>

Proposed title: <span style="font-size:150%">Temperature Color Schemes</span>

==Fixed vs. Relative==

[[Jmol]] offers two methods for coloring by [[temperature value]]. (For an introduction to the temperature value or B factor, please see [[Temperature value]].)

<center><table cellpadding="2" cellspacing="3"

style="background-color:#f4f0ec;text-align:center;">

<tr style="background-color:#e8e4e0;">

<th>

[[SAT]] colors button

</th>

<th>

[[Jmol#Command_Scripting_Language|Jmol command]]

</th>

<th>

<font color="blue">'''Blue'''</font>

</th>

<th>

<span style="background-color:black;color:white;">&nbsp;White&nbsp;</span>

</th>

<th>

<font color="red">'''Red'''</font>

</th>

</tr><tr>

<td>

temperature, fixed

</td><td>

color fixedTemperature

</td><td>

0

</td><td>

50

</td><td>

100

</td>

</tr><tr>

<td>

temperature, relative

</td><td>

&nbsp;color relativeTemperature*&nbsp;

</td><td>

minimum<br>value

</td><td>

&nbsp;unclear&nbsp;

</td><td>

maximum<br>value

</td>

</tr></table>

<nowiki>*</nowiki>The ''relativeTemperature'' color scheme is the same as the ''temperature'' color scheme.

</center>

==Examples==

<Structure size='350' frame='true' align='right' caption=''

scene='Sandbox7_Eric_Martz/Fixtemp_2-0a/3' />

<table cellpadding="2" cellspacing="6"

style="background-color:#f4f0ec;text-align:center;">

<tr style="background-color:#e8e4e0;">

<th>

Resolution, PDB ID

</th>

<th>

Min

</th>

<th>

Av

</th>

<th>

Rel. White

</th>

<th>

Max

</th>

</tr><tr>

<td>

<scene name='Sandbox7_Eric_Martz/Fixtemp_0-83_a/2'>0.83 Angstroms</scene> [[1cbn]]

</td>

<td>

2

</td>

<td>

5

</td>

<td>

11

</td>

<td>

20

</td>

</tr><tr>

<td>

<scene name='Sandbox7_Eric_Martz/Fixtemp_2-0a/3'>2.0 Angstroms</scene> [[1io1]]

</td>

<td>

4

</td>

<td>

29

</td>

<td>

36

</td>

<td>

68

</td>

</tr><tr>

<td>

<scene name='Sandbox7_Eric_Martz/Fixtemp_3-2_a/1'>3.2 Angstroms</scene> [[1uwb]]

</td>

<td>

10

</td>

<td>

67

</td>

<td>

54

</td>

<td>

100

</td>

</tr><tr>

<td>

<scene name='Sandbox7_Eric_Martz/Fixtemp_4-5a/1'>4.5 Angstroms</scene> [[3a8n]]

</td>

<td>

4

</td>

<td>

107

</td>

<td>

105

</td>

<td>

203

</td>

</tr>

<tr>

<td>

<scene name='Sandbox7_Eric_Martz/Fixtemp_9-0a/1'>9.0 Angstroms</scene> [[3lvh]]

</td>

<td>

50

</td>

<td>

103

</td>

<td>

--

</td>

<td>

328

</td>

</tr></table>

<jmol>

<jmolButton>

<script>select all;color fixedTemperature;set echo echobl;echo Fixed;</script>

<text>Fixed Temperature</text>

</jmolButton>

<jmolButton>

<script>select all;color relativeTemperature;set echo echobl;echo Relative;</script>

<text>Relative Temperature</text>

</jmolButton>

</jmol>

<br><!-- cannot put br within jmol tags -->

<jmol>

<jmolButton>

<script>script "/wiki/images/9/97/TempRangeReset.spt"</script>

<text>Temperature 0-10</text>

</jmolButton>

<jmolButton>

<script>script "/wiki/images/2/28/TempRangeStep.spt"</script>

<text>Add 10</text>

</jmolButton>

</jmol>

Other examples:

*[[2zqp]] 6.0 &Aring; Temperature min/av/max: 328/328/328. Fixed is red; relative is white.

*[[1bdx]] 6.0 &Aring; Temperature min/av/max: 30/30/30. Fixed is light blue; relative is white.

*[[1qd7]] 5.5 &Aring; Temperature min/av/max: 0.0/19/102. Fixed & relative seem identical.